DESeq and GSEA with pre-ranked gene list

[proteomania]

Hi all,

I've been using DESeq for my RNA-Seq differential expression analysis. Now I want to use the DESeq result to generate a ranked-list, which will be used as the input in GSEA. My question is: Should I rank the genes using the fold changes or using the q-values?

Thanks.

[Simon Anders]

How to combine GSEA with RNA-Seq is still unclear and subject to ongoing research. We (and other groups, I suppose) are looking at a couple of options.

If you want something now, try using the moderate log fold change that are now reported by the newest version of DESeq. This is not ideal, and I don't want to even say that it is statistically sound, but it is probably better than using p values or raw fold changes.

[hlestrella]

DESeq and GSEA with pre-ranked gene list

How to combine GSEA with RNA-Seq is still unclear and subject to ongoing research. We (and other groups, I suppose) are looking at a couple of options.

I'm also interested in using RNA-Seq differential expression results as a ranked list into GSEA. Any new thoughts since last August on more appropriately ranking the genes coming out of DE analysis for GSEA (or other gene enrichment analyses)?

[maxUlysse]

Have you looked into SeqGSEA ?
cf : http://bioinformatics.oxfordjournals...tu090.abstract

[apredeus]

How to combine GSEA with RNA-Seq is still unclear and subject to ongoing research. We (and other groups, I suppose) are looking at a couple of options.

If you want something now, try using the moderate log fold change that are now reported by the newest version of DESeq. This is not ideal, and I don't want to even say that it is statistically sound, but it is probably better than using p values or raw fold changes.

Hello Simon,

since this is such an old post, I figured I'd ask if there were any advances on the issue - either from your group or anybody else?

I've tried few things but I quite come up with a criterion about what's working and what's not. Is using Wald statistic in pre-ranked GSEA a bad idea?

Thank you for any input in advance.

[apredeus]

Have you looked into SeqGSEA ?
cf : http://bioinformatics.oxfordjournals...tu090.abstract

This is good, but it kind of forces you to use their own differential expression analysis. I would like to stick with DESeq2, and then use the results in GSEA.

[turnersd]

(Old post, but folks are still watching, still high google rank.)

[Michael Love]

I haven't done any testing on what output is best for downstream set analysis. I recently wrote a post on Bioc support site on how to produce a discrete output (yes/no DE) from DESeq2 for use with the Bioc package goseq. Another option would be to use the moderated LFC or Wald statistic as a continuous signal.